Related papers: piBUSS: a parallel BEAST/BEAGLE utility for sequen…
PyamilySeq is a Python-based tool designed for interpretable gene clustering and pangenomic inference, supporting analyses at both species and genus levels. It facilitates the clustering of gene sequences into families based on sequence…
The introduction of large language models and other influential developments in AI-based language processing have led to an evolution in the methods available to quantitatively analyse language data. With the resultant growth of attention…
Nuclear quantum effects (NQEs) play an essential role in many atomistic systems, yet their explicit inclusion in molecular simulations remains challenging. Path-integral molecular dynamics (PIMD) provides a rigorous framework for…
We have built PRISM, a "Probabilistic Regression Instrument for Simulating Models". PRISM uses the Bayes linear approach and history matching to construct an approximation ('emulator') of any given model, by combining limited model…
We present megas, a new software tool that improves the simulation of the Micromegas gas detectors. Our tool offers the possibility to configure multiple arrangements with one or more layers of MM detectors. A series of simple commands can…
In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of…
PHYSBO (optimization tools for PHYSics based on Bayesian Optimization) is a Python library for fast and scalable Bayesian optimization. It has been developed mainly for application in the basic sciences such as physics and materials…
Optimization is key to solve many problems in computational biology. Global optimization methods provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
Electronic circuit behavioral models built with hardware description/modeling languages such as Verilog-AMS for system-level simulations are typically functional models. They do not capture the physical design (layout) information of the…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Summary: GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarisation and visualisation tool that can be applied to large functional enrichment analysis (FEA) results arising from upstream FEA pipelines.…
The unknown parameters of simulation models often need to be calibrated using observed data. When simulation models are expensive, calibration is usually carried out with an emulator. The effectiveness of the calibration process can be…
Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a…
BPEC is an R package for Bayesian Phylogeographic and Ecological Clustering which allows geographical, environmental and phenotypic measurements to be combined with DNA sequences in order to reveal clustered structure resulting from…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
While modern biotechnologies allow synthesizing new proteins and function measurements at scale, efficiently exploring a protein sequence space and engineering it remains a daunting task due to the vast sequence space of any given protein.…
Unified Medical Image Segmentation (UMIS) is critical for comprehensive anatomical assessment but faces challenges due to multi-scale structural heterogeneity. Conventional pixel-based approaches, lacking object-level anatomical insight and…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is…